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16-01-2024 | Brain Tumor | Research

Reliable detection of genetic alterations in cyst fluid DNA for the diagnosis of brain tumors

Authors: Jotaro On, Manabu Natsumeda, Haruhiko Takahashi, Akihide Koyama, Satoshi Shibuma, Nao Shibata, Jun Watanabe, Shoji Saito, Yu Kanemaru, Yoshihiro Tsukamoto, Masayasu Okada, Ryosuke Ogura, Takeyoshi Eda, Mari Tada, Hiroshi Shimizu, Jun-ichi Adachi, Kazuhiko Mishima, Ryo Nishikawa, Akiyoshi Kakita, Makoto Oishi

Published in: Journal of Neuro-Oncology | Issue 2/2024

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Abstract

Purpose

Liquid biopsy of cyst fluid in brain tumors has not been extensively studied to date. The present study was performed to see whether diagnostic genetic alterations found in brain tumor tissue DNA could also be detected in cell-free DNA (cfDNA) of cyst fluid in cystic brain tumors.

Methods

Cyst fluid was obtained from 22 patients undergoing surgery for a cystic brain tumor with confirmed genetic alterations in tumor DNA. Pathological diagnoses based on WHO 2021 classification and diagnostic alterations in the tumor DNA, such as IDH1 R132H and TERT promoter mutation for oligodendrogliomas, were detected by Sanger sequencing. The same alterations were analyzed by both droplet digital PCR (ddPCR) and Sanger sequencing in cyst fluid cfDNA. Additionally, multiplex ligation-dependent probe amplification (MLPA) assays were performed to assess 1p/19q status, presence of CDKN2A loss, PTEN loss and EGFR amplification, to assess whether differentiating between astrocytomas and oligodendrogliomas and grading is possible from cyst fluid cfDNA.

Results

Twenty-five genetic alterations were found in 22 tumor samples. All (100%) alterations were detected in cyst fluid cfDNA by ddPCR. Twenty of the 25 (80%) alterations were also detected by Sanger sequencing of cyst fluid cfDNA. Variant allele frequency (VAF) in cyst fluid cfDNA was comparable to that of tumor DNA (R = 0.62, Pearson’s correlation). MLPA was feasible in 11 out of 17 (65%) diffuse gliomas, with close correlation of results between tumor DNA and cyst fluid cfDNA.

Conclusion

Cell-free DNA obtained from cyst fluid in cystic brain tumors is a reliable alternative to tumor DNA when diagnosing brain tumors.
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Metadata
Title
Reliable detection of genetic alterations in cyst fluid DNA for the diagnosis of brain tumors
Authors
Jotaro On
Manabu Natsumeda
Haruhiko Takahashi
Akihide Koyama
Satoshi Shibuma
Nao Shibata
Jun Watanabe
Shoji Saito
Yu Kanemaru
Yoshihiro Tsukamoto
Masayasu Okada
Ryosuke Ogura
Takeyoshi Eda
Mari Tada
Hiroshi Shimizu
Jun-ichi Adachi
Kazuhiko Mishima
Ryo Nishikawa
Akiyoshi Kakita
Makoto Oishi
Publication date
16-01-2024
Publisher
Springer US
Published in
Journal of Neuro-Oncology / Issue 2/2024
Print ISSN: 0167-594X
Electronic ISSN: 1573-7373
DOI
https://doi.org/10.1007/s11060-023-04555-5

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